Query custom taxonomy by term id?

This is not supported by default, but you can convert the numeric terms back to slugs with the pre_get_posts hook. I tested this with WP 3.0.1, but in 3.1 the taxonomy query handling changed, so I don’t know whether this will work by default or if there is a better way to do it.

add_action( 'pre_get_posts', 'wpse6066_pre_get_posts' );
function wpse6066_pre_get_posts( &$wp_query )
{
    if ( $wp_query->is_tax ) {
        if ( is_numeric( $wp_query->get( 'term' ) ) ) {
            // Convert numberic terms to term slugs
            $term = get_term_by( 'term_id', $wp_query->get( 'term' ), $wp_query->get( 'taxonomy' ) );
            if ( $term ) {
                $wp_query->set( 'term', $term->slug );
            }
        }
    }
}

Bizarre that you prefer the numeric version, many would choose the term slug for SEO reasons.